<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<title>MolTK C++ API: moltk::Biosequence Class Reference</title>

<link href="tabs.css" rel="stylesheet" type="text/css"/>
<link href="doxygen.css" rel="stylesheet" type="text/css" />

<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/javascript">
  $(document).ready(function() { searchBox.OnSelectItem(0); });
</script>

</head>
<body>
<div id="top"><!-- do not remove this div! -->


<div id="titlearea">
<table cellspacing="0" cellpadding="0">
 <tbody>
 <tr style="height: 56px;">
  
  <td id="projectlogo"><img alt="Logo" src="moltk55.png"/></td>
  
  
  <td style="padding-left: 0.5em;">
   <div id="projectname">MolTK C++ API
   &#160;<span id="projectnumber">0.4.0</span>
   </div>
   
  </td>
  
  
  
 </tr>
 </tbody>
</table>
</div>

<!-- Generated by Doxygen 1.7.5.1 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
  <div id="navrow1" class="tabs">
    <ul class="tablist">
      <li><a href="index.html"><span>Main&#160;Page</span></a></li>
      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
      <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
      <li><a href="files.html"><span>Files</span></a></li>
      <li>
        <div id="MSearchBox" class="MSearchBoxInactive">
        <span class="left">
          <img id="MSearchSelect" src="search/mag_sel.png"
               onmouseover="return searchBox.OnSearchSelectShow()"
               onmouseout="return searchBox.OnSearchSelectHide()"
               alt=""/>
          <input type="text" id="MSearchField" value="Search" accesskey="S"
               onfocus="searchBox.OnSearchFieldFocus(true)" 
               onblur="searchBox.OnSearchFieldFocus(false)" 
               onkeyup="searchBox.OnSearchFieldChange(event)"/>
          </span><span class="right">
            <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
          </span>
        </div>
      </li>
    </ul>
  </div>
  <div id="navrow2" class="tabs2">
    <ul class="tablist">
      <li><a href="annotated.html"><span>Class&#160;List</span></a></li>
      <li><a href="classes.html"><span>Class&#160;Index</span></a></li>
      <li><a href="inherits.html"><span>Class&#160;Hierarchy</span></a></li>
      <li><a href="functions.html"><span>Class&#160;Members</span></a></li>
    </ul>
  </div>
  <div id="nav-path" class="navpath">
    <ul>
      <li class="navelem"><a class="el" href="namespacemoltk.html">moltk</a>      </li>
      <li class="navelem"><a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a>      </li>
    </ul>
  </div>
</div>
<div class="header">
  <div class="summary">
<a href="#pub-types">Public Types</a> &#124;
<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="#pro-attribs">Protected Attributes</a> &#124;
<a href="#friends">Friends</a>  </div>
  <div class="headertitle">
<div class="title">moltk::Biosequence Class Reference</div>  </div>
</div>
<div class="contents">
<!-- doxytag: class="moltk::Biosequence" --><!-- doxytag: inherits="moltk::BaseBiosequence,std::vector" -->
<p>A macromolecule sequence (DNA or RNA or protein)  
 <a href="classmoltk_1_1Biosequence.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="Biosequence_8hpp_source.html">Biosequence.hpp</a>&gt;</code></p>
<div class="dynheader">
Inheritance diagram for moltk::Biosequence:</div>
<div class="dyncontent">
<div class="center"><img src="classmoltk_1_1Biosequence__inherit__graph.png" border="0" usemap="#moltk_1_1Biosequence_inherit__map" alt="Inheritance graph"/></div>
<map name="moltk_1_1Biosequence_inherit__map" id="moltk_1_1Biosequence_inherit__map">
<area shape="rect" id="node2" href="classmoltk_1_1BaseBiosequence.html" title="Parent class for macromolecule sequences and structures." alt="" coords="5,5,171,32"/><area shape="rect" id="node4" title="STL class." alt="" coords="195,5,423,32"/></map>
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>
<div class="dynheader">
Collaboration diagram for moltk::Biosequence:</div>
<div class="dyncontent">
<div class="center"><img src="classmoltk_1_1Biosequence__coll__graph.png" border="0" usemap="#moltk_1_1Biosequence_coll__map" alt="Collaboration graph"/></div>
<map name="moltk_1_1Biosequence_coll__map" id="moltk_1_1Biosequence_coll__map">
<area shape="rect" id="node2" href="classmoltk_1_1BaseBiosequence.html" title="Parent class for macromolecule sequences and structures." alt="" coords="5,83,171,109"/><area shape="rect" id="node4" title="STL class." alt="" coords="195,83,423,109"/><area shape="rect" id="node6" title="STL class." alt="" coords="448,83,528,109"/><area shape="rect" id="node8" title="STL class." alt="" coords="405,5,571,32"/></map>
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>

<p><a href="classmoltk_1_1Biosequence-members.html">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classmoltk_1_1BiosequenceResidue.html">BiosequenceResidue</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#ad5da6959d153abf84e135e4f21e68a8d">Residue</a></td></tr>
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#aee6ad5187962781881788888f69167fb">Biosequence</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a6201adf152e6fe433ce97ca17fd07211">Biosequence</a> (const std::string &amp;sequence, const std::string &amp;<a class="el" href="classmoltk_1_1Biosequence.html#a686fd896dd4c0996dcd7c98368178bc9">description</a>=&quot;&quot;)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a549ec19e3cf8e09f9bcb402bb6728a6f">Biosequence</a> (const char *sequence, const std::string &amp;<a class="el" href="classmoltk_1_1Biosequence.html#a686fd896dd4c0996dcd7c98368178bc9">description</a>=&quot;&quot;)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a28917bc01df6b7d3fa995476b7258404">Biosequence</a> (const <a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &amp;rhs)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a2fe7b008000e37c494f64d720651b165">~Biosequence</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a9ed5ae7e9926b9b1034fdad564a56dcd">load_stream</a> (std::istream &amp;is)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a44a245f0fe1ad46f81c2d1fb243b0bec">load_fasta</a> (const std::string &amp;file_name)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a4ffb7ea7260285d41d360ff7229e7f8e">load_fasta</a> (std::istream &amp;is)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#ac990688fe005304a3dd512a616017c71">get_number_of_residues</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classmoltk_1_1Biosequence.html#ad5da6959d153abf84e135e4f21e68a8d">Residue</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a7347126c11c30536dfc3b0214f0dcc44">get_residue</a> (size_t ix) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a8290cae93ff500228664fbb4666777a3">get_description</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a443c6178002614e5dc4215360cd5d206">write_fasta</a> (std::ostream &amp;os) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Write sequence in fasta format to a C++ stream.  <a href="#a443c6178002614e5dc4215360cd5d206"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#afe8bf9a3ac2efbea3f1a63137bce682f">write_fasta</a> (const std::string &amp;file_name) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Write sequence in fasta format to a designated file.  <a href="#afe8bf9a3ac2efbea3f1a63137bce682f"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a27052034d07465e3f009d621e6545fae">fasta</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Create a string representing the sequence in fasta format.  <a href="#a27052034d07465e3f009d621e6545fae"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a8f94aee2ef34bfdd3886d8545e0b1d7c">write_sequence_string</a> (std::ostream &amp;os) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Write a sequence string to a C++ stream.  <a href="#a8f94aee2ef34bfdd3886d8545e0b1d7c"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a30c32f6a3ce92b1b33dbd911653136d7">repr</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">repr is a helper for the python __repr__ method.  <a href="#a30c32f6a3ce92b1b33dbd911653136d7"></a><br/></td></tr>
<tr><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a686fd896dd4c0996dcd7c98368178bc9">description</a></td></tr>
<tr><td colspan="2"><h2><a name="friends"></a>
Friends</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::ostream &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a71b3d56cc0f8f3c90957efd3592ddd0b">operator&lt;&lt;</a> (std::ostream &amp;os, const <a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &amp;seq)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::istream &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Biosequence.html#a8e8f8370f1a4769c9ce2e6ae0f44fa1e">operator&gt;&gt;</a> (std::istream &amp;is, <a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &amp;seq)</td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>A macromolecule sequence (DNA or RNA or protein) </p>
</div><hr/><h2>Member Typedef Documentation</h2>
<a class="anchor" id="ad5da6959d153abf84e135e4f21e68a8d"></a><!-- doxytag: member="moltk::Biosequence::Residue" ref="ad5da6959d153abf84e135e4f21e68a8d" args="" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">typedef <a class="el" href="classmoltk_1_1BiosequenceResidue.html">BiosequenceResidue</a> <a class="el" href="classmoltk_1_1Biosequence.html#ad5da6959d153abf84e135e4f21e68a8d">moltk::Biosequence::Residue</a></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<hr/><h2>Constructor &amp; Destructor Documentation</h2>
<a class="anchor" id="aee6ad5187962781881788888f69167fb"></a><!-- doxytag: member="moltk::Biosequence::Biosequence" ref="aee6ad5187962781881788888f69167fb" args="()" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">moltk::Biosequence::Biosequence </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td><code> [inline]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="a6201adf152e6fe433ce97ca17fd07211"></a><!-- doxytag: member="moltk::Biosequence::Biosequence" ref="a6201adf152e6fe433ce97ca17fd07211" args="(const std::string &amp;sequence, const std::string &amp;description=&quot;&quot;)" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">moltk::Biosequence::Biosequence </td>
          <td>(</td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>sequence</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>description</em> = <code>&quot;&quot;</code>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="a549ec19e3cf8e09f9bcb402bb6728a6f"></a><!-- doxytag: member="moltk::Biosequence::Biosequence" ref="a549ec19e3cf8e09f9bcb402bb6728a6f" args="(const char *sequence, const std::string &amp;description=&quot;&quot;)" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">moltk::Biosequence::Biosequence </td>
          <td>(</td>
          <td class="paramtype">const char *&#160;</td>
          <td class="paramname"><em>sequence</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>description</em> = <code>&quot;&quot;</code>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="a28917bc01df6b7d3fa995476b7258404"></a><!-- doxytag: member="moltk::Biosequence::Biosequence" ref="a28917bc01df6b7d3fa995476b7258404" args="(const Biosequence &amp;rhs)" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">moltk::Biosequence::Biosequence </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &amp;&#160;</td>
          <td class="paramname"><em>rhs</em></td><td>)</td>
          <td></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="a2fe7b008000e37c494f64d720651b165"></a><!-- doxytag: member="moltk::Biosequence::~Biosequence" ref="a2fe7b008000e37c494f64d720651b165" args="()" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">virtual moltk::Biosequence::~Biosequence </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td><code> [inline, virtual]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a27052034d07465e3f009d621e6545fae"></a><!-- doxytag: member="moltk::Biosequence::fasta" ref="a27052034d07465e3f009d621e6545fae" args="() const " -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">std::string moltk::Biosequence::fasta </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Create a string representing the sequence in fasta format. </p>

</div>
</div>
<a class="anchor" id="a8290cae93ff500228664fbb4666777a3"></a><!-- doxytag: member="moltk::Biosequence::get_description" ref="a8290cae93ff500228664fbb4666777a3" args="() const " -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">std::string moltk::Biosequence::get_description </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [inline]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="ac990688fe005304a3dd512a616017c71"></a><!-- doxytag: member="moltk::Biosequence::get_number_of_residues" ref="ac990688fe005304a3dd512a616017c71" args="() const " -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">size_t moltk::Biosequence::get_number_of_residues </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [inline, virtual]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Implements <a class="el" href="classmoltk_1_1BaseBiosequence.html#a837f45a8604c435855b00aa90ace5841">moltk::BaseBiosequence</a>.</p>

</div>
</div>
<a class="anchor" id="a7347126c11c30536dfc3b0214f0dcc44"></a><!-- doxytag: member="moltk::Biosequence::get_residue" ref="a7347126c11c30536dfc3b0214f0dcc44" args="(size_t ix) const " -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">const <a class="el" href="classmoltk_1_1Biosequence.html#ad5da6959d153abf84e135e4f21e68a8d">Residue</a>&amp; moltk::Biosequence::get_residue </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>ix</em></td><td>)</td>
          <td> const<code> [inline, virtual]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Implements <a class="el" href="classmoltk_1_1BaseBiosequence.html#ae966c9bf162db00c2d5a4898170538af">moltk::BaseBiosequence</a>.</p>

</div>
</div>
<a class="anchor" id="a44a245f0fe1ad46f81c2d1fb243b0bec"></a><!-- doxytag: member="moltk::Biosequence::load_fasta" ref="a44a245f0fe1ad46f81c2d1fb243b0bec" args="(const std::string &amp;file_name)" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname"><a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a>&amp; moltk::Biosequence::load_fasta </td>
          <td>(</td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>file_name</em></td><td>)</td>
          <td></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="a4ffb7ea7260285d41d360ff7229e7f8e"></a><!-- doxytag: member="moltk::Biosequence::load_fasta" ref="a4ffb7ea7260285d41d360ff7229e7f8e" args="(std::istream &amp;is)" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname"><a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a>&amp; moltk::Biosequence::load_fasta </td>
          <td>(</td>
          <td class="paramtype">std::istream &amp;&#160;</td>
          <td class="paramname"><em>is</em></td><td>)</td>
          <td></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="a9ed5ae7e9926b9b1034fdad564a56dcd"></a><!-- doxytag: member="moltk::Biosequence::load_stream" ref="a9ed5ae7e9926b9b1034fdad564a56dcd" args="(std::istream &amp;is)" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">void moltk::Biosequence::load_stream </td>
          <td>(</td>
          <td class="paramtype">std::istream &amp;&#160;</td>
          <td class="paramname"><em>is</em></td><td>)</td>
          <td></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="a30c32f6a3ce92b1b33dbd911653136d7"></a><!-- doxytag: member="moltk::Biosequence::repr" ref="a30c32f6a3ce92b1b33dbd911653136d7" args="() const " -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">std::string moltk::Biosequence::repr </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>repr is a helper for the python __repr__ method. </p>

</div>
</div>
<a class="anchor" id="a443c6178002614e5dc4215360cd5d206"></a><!-- doxytag: member="moltk::Biosequence::write_fasta" ref="a443c6178002614e5dc4215360cd5d206" args="(std::ostream &amp;os) const " -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">void moltk::Biosequence::write_fasta </td>
          <td>(</td>
          <td class="paramtype">std::ostream &amp;&#160;</td>
          <td class="paramname"><em>os</em></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Write sequence in fasta format to a C++ stream. </p>

</div>
</div>
<a class="anchor" id="afe8bf9a3ac2efbea3f1a63137bce682f"></a><!-- doxytag: member="moltk::Biosequence::write_fasta" ref="afe8bf9a3ac2efbea3f1a63137bce682f" args="(const std::string &amp;file_name) const " -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">void moltk::Biosequence::write_fasta </td>
          <td>(</td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>file_name</em></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Write sequence in fasta format to a designated file. </p>

</div>
</div>
<a class="anchor" id="a8f94aee2ef34bfdd3886d8545e0b1d7c"></a><!-- doxytag: member="moltk::Biosequence::write_sequence_string" ref="a8f94aee2ef34bfdd3886d8545e0b1d7c" args="(std::ostream &amp;os) const " -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">void moltk::Biosequence::write_sequence_string </td>
          <td>(</td>
          <td class="paramtype">std::ostream &amp;&#160;</td>
          <td class="paramname"><em>os</em></td><td>)</td>
          <td> const</td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Write a sequence string to a C++ stream. </p>
<p>The sequence description is NOT included. </p>

</div>
</div>
<hr/><h2>Friends And Related Function Documentation</h2>
<a class="anchor" id="a71b3d56cc0f8f3c90957efd3592ddd0b"></a><!-- doxytag: member="moltk::Biosequence::operator&lt;&lt;" ref="a71b3d56cc0f8f3c90957efd3592ddd0b" args="(std::ostream &amp;os, const Biosequence &amp;seq)" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">std::ostream&amp; operator&lt;&lt; </td>
          <td>(</td>
          <td class="paramtype">std::ostream &amp;&#160;</td>
          <td class="paramname"><em>os</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &amp;&#160;</td>
          <td class="paramname"><em>seq</em>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td><code> [friend]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<a class="anchor" id="a8e8f8370f1a4769c9ce2e6ae0f44fa1e"></a><!-- doxytag: member="moltk::Biosequence::operator&gt;&gt;" ref="a8e8f8370f1a4769c9ce2e6ae0f44fa1e" args="(std::istream &amp;is, Biosequence &amp;seq)" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">std::istream&amp; operator&gt;&gt; </td>
          <td>(</td>
          <td class="paramtype">std::istream &amp;&#160;</td>
          <td class="paramname"><em>is</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &amp;&#160;</td>
          <td class="paramname"><em>seq</em>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td><code> [friend]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="a686fd896dd4c0996dcd7c98368178bc9"></a><!-- doxytag: member="moltk::Biosequence::description" ref="a686fd896dd4c0996dcd7c98368178bc9" args="" -->
<div class="memitem">
<div class="memproto">
      <table class="memname">
        <tr>
          <td class="memname">std::string <a class="el" href="classmoltk_1_1Biosequence.html#a686fd896dd4c0996dcd7c98368178bc9">moltk::Biosequence::description</a><code> [protected]</code></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>moltk/<a class="el" href="Biosequence_8hpp_source.html">Biosequence.hpp</a></li>
</ul>
</div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
     onmouseover="return searchBox.OnSearchSelectShow()"
     onmouseout="return searchBox.OnSearchSelectHide()"
     onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark">&#160;</span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark">&#160;</span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark">&#160;</span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark">&#160;</span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark">&#160;</span>Friends</a></div>

<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0" 
        name="MSearchResults" id="MSearchResults">
</iframe>
</div>



<hr class="footer"/><address class="footer"><small>
Generated by &#160;<a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.7.5.1
</small></address>

</body>
</html>
